Considerations in Bayesian agent-based modeling for the analysis of COVID-19 data

TL;DR

This paper develops a Bayesian agent-based modeling approach for COVID-19 transmission analysis, treating the system as a Hidden Markov Model and using particle MCMC for inference, demonstrated on cruise ship data.

Contribution

It introduces a Bayesian framework for ABMs of infectious diseases, addressing likelihood intractability with particle MCMC and applying it to real COVID-19 data.

Findings

Effective parameter recovery demonstrated in simulations

Insights into demographic transmission differences on cruise ship

Sensitivity analysis highlights prior assumptions impact

Abstract

Agent-based model (ABM) has been widely used to study infectious disease transmission by simulating behaviors and interactions of autonomous individuals called agents. In the ABM, agent states, for example infected or susceptible, are assigned according to a set of simple rules, and a complex dynamics of disease transmission is described by the collective states of agents over time. Despite the flexibility in real-world modeling, ABMs have received less attention by statisticians because of the intractable likelihood functions which lead to difficulty in estimating parameters and quantifying uncertainty around model outputs. To overcome this limitation, we propose to treat the entire system as a Hidden Markov Model and develop the ABM for infectious disease transmission within the Bayesian framework. The hidden states in the model are represented by individual agent's states over time. We estimate the hidden states and the parameters associated with the model by applying particle Markov Chain Monte Carlo algorithm. Performance of the approach for parameter recovery and prediction along with sensitivity to prior assumptions are evaluated under various simulation conditions. Finally, we apply the proposed approach to the study of COVID-19 outbreak on Diamond Princess cruise ship and examine the differences in transmission by key demographic characteristics, while considering different network structures and the limitations of COVID-19 testing in the cruise.